annofix.ipynb

{"cells":[{"metadata":{"trusted":true},"cell_type":"code","source":"%%bash\n\ncat house_sparrow_genome_assembly-18-11-14_masked.fa.fai | awk '{ print $1 }' > chrmnames.txt\n\ncat GCA_001700915.1_Passer_domesticus-1.0_genomic.fasta.fai | awk '{ print $1 }' > chrmnamesnew.txt\n\ncat annotation.gff | sed 's/\\t/,/' > anno.csv\n\ncat annotation.gff | awk '{ print $1 }' > anno.txt\n\ncat annotation.gff | head","execution_count":2,"outputs":[{"output_type":"stream","text":"scaffold00512\tmaker\tgene\t43165\t46212\t.\t+\t.\tID=IV00_00054867;Name=IV00_00054867;Alias=maker-scaffold00512-augustus-gene-0.21;Note=Similar to RRAD: GTP-binding protein RAD (Homo sapiens);\nscaffold00512\tmaker\tmRNA\t43165\t46212\t.\t+\t.\tID=IV00_00054867-RA;Parent=IV00_00054867;Name=IV00_00054867-RA;Alias=maker-scaffold00512-augustus-gene-0.21-mRNA-1;_AED=0.02;_QI=0|0|0|1|1|1|4|0|296;_eAED=0.02;Note=Similar to RRAD: GTP-binding protein RAD (Homo sapiens);\nscaffold00512\tmaker\texon\t43165\t43498\t.\t+\t.\tID=IV00_00054867-RA:exon:2371;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\texon\t43627\t43700\t.\t+\t.\tID=IV00_00054867-RA:exon:2372;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\texon\t44201\t44405\t.\t+\t.\tID=IV00_00054867-RA:exon:2373;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\texon\t45935\t46212\t.\t+\t.\tID=IV00_00054867-RA:exon:2374;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t43165\t43498\t.\t+\t0\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t43627\t43700\t.\t+\t2\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t44201\t44405\t.\t+\t0\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t45935\t46212\t.\t+\t2\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\n","name":"stdout"}]},{"metadata":{"trusted":true},"cell_type":"code","source":"#First convert the two fasta indices into lists\nimport numpy as np\nimport pandas as pd\n\ndf1 = pd.read_csv(\"chrmnames.txt\", header = None)\n\ndf2 = pd.read_csv(\"chrmnamesnew.txt\", header = None)\n\nanno = pd.read_csv(\"anno.txt\", header = None)\nanno","execution_count":3,"outputs":[{"output_type":"execute_result","execution_count":3,"data":{"text/plain":"                    0\n0       scaffold00512\n1       scaffold00512\n2       scaffold00512\n3       scaffold00512\n4       scaffold00512\n...               ...\n269121  scaffold00442\n269122  scaffold00442\n269123  scaffold00442\n269124  scaffold00442\n269125  scaffold00442\n\n[269126 rows x 1 columns]","text/html":"<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>0</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>0</th>\n      <td>scaffold00512</td>\n    </tr>\n    <tr>\n      <th>1</th>\n      <td>scaffold00512</td>\n    </tr>\n    <tr>\n      <th>2</th>\n      <td>scaffold00512</td>\n    </tr>\n    <tr>\n      <th>3</th>\n      <td>scaffold00512</td>\n    </tr>\n    <tr>\n      <th>4</th>\n      <td>scaffold00512</td>\n    </tr>\n    <tr>\n      <th>...</th>\n      <td>...</td>\n    </tr>\n    <tr>\n      <th>269121</th>\n      <td>scaffold00442</td>\n    </tr>\n    <tr>\n      <th>269122</th>\n      <td>scaffold00442</td>\n    </tr>\n    <tr>\n      <th>269123</th>\n      <td>scaffold00442</td>\n    </tr>\n    <tr>\n      <th>269124</th>\n      <td>scaffold00442</td>\n    </tr>\n    <tr>\n      <th>269125</th>\n      <td>scaffold00442</td>\n    </tr>\n  </tbody>\n</table>\n<p>269126 rows × 1 columns</p>\n</div>"},"metadata":{}}]},{"metadata":{"trusted":true},"cell_type":"code","source":"chrm = df1.iloc[:, 0].tolist()","execution_count":4,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"chrmnew = df2.iloc[:, 0].tolist()\n\nannochrm = anno.iloc[:,0]\n\nchrmdict = dict(zip(chrm, chrmnew))\nannochrm2 = annochrm.iloc[0:1000,]\nannochrm2","execution_count":5,"outputs":[{"output_type":"execute_result","execution_count":5,"data":{"text/plain":"0      scaffold00512\n1      scaffold00512\n2      scaffold00512\n3      scaffold00512\n4      scaffold00512\n           ...      \n995             chr9\n996             chr9\n997             chr9\n998             chr9\n999             chr9\nName: 0, Length: 1000, dtype: object"},"metadata":{}}]},{"metadata":{"trusted":true},"cell_type":"code","source":"\nannonew = annochrm.replace(chrmdict, regex=False)","execution_count":6,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"annonew","execution_count":7,"outputs":[{"output_type":"execute_result","execution_count":7,"data":{"text/plain":"0         MBAE01000501.1\n1         MBAE01000501.1\n2         MBAE01000501.1\n3         MBAE01000501.1\n4         MBAE01000501.1\n               ...      \n269121    MBAE01000432.1\n269122    MBAE01000432.1\n269123    MBAE01000432.1\n269124    MBAE01000432.1\n269125    MBAE01000432.1\nName: 0, Length: 269126, dtype: object"},"metadata":{}}]},{"metadata":{"trusted":true},"cell_type":"code","source":"annonew.to_csv('annonew.txt', header=None, index=None, sep = \" \")","execution_count":8,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"cat annonew.txt | awk '{ gsub(/ /,\"\"); print }' > annonew1.txt","execution_count":16,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"#%%bash\n#awk 'BEGIN {FS=OFS=\"|\"}NR == FNR {a[FNR] = $B;next}{$A = a[FNR];print $0}' B=1 A=1 annonew.csv anno.csv > annofixed.txt","execution_count":11,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"%%bash\n\nawk 'FNR==NR{a[NR]=$1;next}{$1=a[FNR]}1' annonew1.txt annotation.gff | sed 's/ /\\t/' > annotations_namesfixed.gff","execution_count":17,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"cat annotations_namesfixed.gff | awk '{ gsub(/\\t/,\" \"); print }'| awk '{ gsub(/ /,\"\\t\"); print }' > annotations_namesfixed_tabsep.gff","execution_count":22,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"cat annotations_namesfixed_tabsep.gff | head","execution_count":24,"outputs":[{"output_type":"stream","text":"MBAE01000501.1\tmaker\tgene\t43165\t46212\t.\t+\t.\tID=IV00_00054867;Name=IV00_00054867;Alias=maker-scaffold00512-augustus-gene-0.21;Note=Similar\tto\tRRAD:\tGTP-binding\tprotein\tRAD\t(Homo\tsapiens);\r\nMBAE01000501.1\tmaker\tmRNA\t43165\t46212\t.\t+\t.\tID=IV00_00054867-RA;Parent=IV00_00054867;Name=IV00_00054867-RA;Alias=maker-scaffold00512-augustus-gene-0.21-mRNA-1;_AED=0.02;_QI=0|0|0|1|1|1|4|0|296;_eAED=0.02;Note=Similar\tto\tRRAD:\tGTP-binding\tprotein\tRAD\t(Homo\tsapiens);\r\nMBAE01000501.1\tmaker\texon\t43165\t43498\t.\t+\t.\tID=IV00_00054867-RA:exon:2371;Parent=IV00_00054867-RA;\r\nMBAE01000501.1\tmaker\texon\t43627\t43700\t.\t+\t.\tID=IV00_00054867-RA:exon:2372;Parent=IV00_00054867-RA;\r\nMBAE01000501.1\tmaker\texon\t44201\t44405\t.\t+\t.\tID=IV00_00054867-RA:exon:2373;Parent=IV00_00054867-RA;\r\nMBAE01000501.1\tmaker\texon\t45935\t46212\t.\t+\t.\tID=IV00_00054867-RA:exon:2374;Parent=IV00_00054867-RA;\r\nMBAE01000501.1\tmaker\tCDS\t43165\t43498\t.\t+\t0\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\r\nMBAE01000501.1\tmaker\tCDS\t43627\t43700\t.\t+\t2\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\r\nMBAE01000501.1\tmaker\tCDS\t44201\t44405\t.\t+\t0\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\r\nMBAE01000501.1\tmaker\tCDS\t45935\t46212\t.\t+\t2\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\r\ncat: write error: Broken pipe\r\n","name":"stdout"}]},{"metadata":{"trusted":true},"cell_type":"code","source":"%%bash\n#Compare to original file:\ncat annotation.gff | head","execution_count":27,"outputs":[{"output_type":"stream","text":"scaffold00512\tmaker\tgene\t43165\t46212\t.\t+\t.\tID=IV00_00054867;Name=IV00_00054867;Alias=maker-scaffold00512-augustus-gene-0.21;Note=Similar to RRAD: GTP-binding protein RAD (Homo sapiens);\nscaffold00512\tmaker\tmRNA\t43165\t46212\t.\t+\t.\tID=IV00_00054867-RA;Parent=IV00_00054867;Name=IV00_00054867-RA;Alias=maker-scaffold00512-augustus-gene-0.21-mRNA-1;_AED=0.02;_QI=0|0|0|1|1|1|4|0|296;_eAED=0.02;Note=Similar to RRAD: GTP-binding protein RAD (Homo sapiens);\nscaffold00512\tmaker\texon\t43165\t43498\t.\t+\t.\tID=IV00_00054867-RA:exon:2371;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\texon\t43627\t43700\t.\t+\t.\tID=IV00_00054867-RA:exon:2372;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\texon\t44201\t44405\t.\t+\t.\tID=IV00_00054867-RA:exon:2373;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\texon\t45935\t46212\t.\t+\t.\tID=IV00_00054867-RA:exon:2374;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t43165\t43498\t.\t+\t0\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t43627\t43700\t.\t+\t2\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t44201\t44405\t.\t+\t0\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\nscaffold00512\tmaker\tCDS\t45935\t46212\t.\t+\t2\tID=IV00_00054867-RA:cds;Parent=IV00_00054867-RA;\n","name":"stdout"}]},{"metadata":{"trusted":true},"cell_type":"code","source":"","execution_count":null,"outputs":[]}],"metadata":{"kernelspec":{"name":"python3","display_name":"Python 3","language":"python"},"language_info":{"name":"python","version":"3.7.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat":4,"nbformat_minor":4}