Re^2: Comparing and getting information from two large files and appending it in a new file

in reply to Re: Comparing and getting information from two large files and appending it in a new file
in thread Comparing and getting information from two large files and appending it in a new file

The lines of the First file are long so they are being printed in multiple lines. Previously I only gave one line now I am including many lines in the following file sample for file 1 I hope file2 format is understandable.


 Gm10    Glyma10g00200.1    CDS_11    8569    8705    -    2    2    6
+    10    14    GAAGAACCAAAATCGCTGATTTTGAAAAATAGGGGGACTGAATGTCTTGATTT
+GGAAATAGGGGGACCAAAATTGCGGATTGAGCATTATAGGGGACCAATAGTGTATTTTAGCCTTTATTT
+TATTTTGAATGTGTG
 Gm10    Glyma10g00200.1    CDS_10    8822    8822    -    0    0    0
+    0    0    G
 Gm10    Glyma10g00200.1    CDS_9    8885    9079    -    2    13    2
+3    38    50    GTATTTGTGTATTGCTCCTGGATCTAGACCTTCCCCTGTTGCTGCTGCTGCT
+GCAAGTCACAAATTAATCACATGTATTTCATGCTTCGATGAGCGTTCACTTGCATATCATGCTGTTGGA
+TATGGAAGAGGATCTCACATTCCAGCAGTAGCCATTACATCATCAGGCACTGCAGTTTCCAACCTTCTT
+CCTGC
 Gm10    Glyma10g00200.1    CDS_8    9151    9255    -    2    2    11
+    15    19    GTTGGATCATGCCAATGAATTATCAAACTCCCTGAAAGAAAGTGCCAATATTA
+ACACTGTTCGGGCATCGCTTATTGTTGAAGAATGCACAAGACTTGGTTTGAT
 Gm10    Glyma10g00200.1    CDS_7    11534    11698    -    1    7    
+16    24    33    GGAATATACTGATCCTCACAAAGGTTCTCTTAACCTTGCTGTGAAGTTGCC
+TAATGGTTCTCTAAAGCCAGACCTGGGGCCAAAAACATATATTGCTTATGGATTTCTTCAGGAGCTTGG
+ACGTGGTGATTCAGTGACTAAGCTCCATTGTGATATGTCTGATGC
 Gm10    Glyma10g00200.1    CDS_6    12777    12823    -    0    0    
+8    8    11    GCTTTTTACACAAATTTCATTCTTCACCTTCATTCTCATGAAGATTA
 Gm10    Glyma10g00200.1    CDS_5    12958    13022    -    1    4    
+4    9    10    GCTGTAGATCTTCAGTACAAGTATTTAAGGCATTTTCAGTGGCATTGGGAAAA
+GGGGGAACCGCT
 Gm10    Glyma10g00200.1    CDS_4    13348    13502    -    0    4    
+20    24    33    GAGGATCCTTATCTTCTTCTTGGGTTCTGAAAAAATAAAAACATCAACTCC
+CTCCTGTATTCATGCTTGGTGTTGGTTATGTGTCATGTCTGGTCTACTATTGACACATGTAAATCCAAA
+TGCACTAGAGCTGCCCTCAAAAAACTCAATTTGGT
 Gm10    Glyma10g00200.1    CDS_3    13713    13829    -    0    2    
+13    15    25    GATTGAGTTAGATGAGCTGGAAAGTGTTTCCATTCTGTCAATGACCCTTGC
+ATGGGATGAATTTTCCTTCTCTACTTTTCAAGAAGCCCATTATTCACTTCAAGATTCTCTAGACCA
 Gm10    Glyma10g00200.1    CDS_2    13915    14209    -    8    11   
+ 40    59    88    GCTGCTCTTCTCCCTCAGCTGCTCTGTCTCCGGCGTTGACATTGGAGGAG
+GGACTTGAGAAACTGAAGGAGGCTCTCCAAATCTTGAATTCTCCTTCCCCTTCTTCCCCTACTGGATTC
+CTTAGGTTTCAGGTGGCGCTCCCTCCCAGTCCTAAGACCTTCACTTTGTTTTGCTCCCAACCCCACTCC
+TCCTCGGTCTTTCCTCTCATTTATGTTTCCAAGAACGACGCCGACTCTAAATCACTCTATGTCAATTTG
+GATGATAATGTGAGTCACCGGAAAGAAAGGTTCTTTTT
 Gm10    Glyma10g00200.1    CDS_1    14242    14286    -    2    1    
+9    12    21    GATCTCGTTCCCCCTCACCACATAACACCCTGTCGTTCCCTTCAC
 Gm10    Glyma10g00210.1    CDS_7    15480    15722    -    4    7    
+26    37    47    GGTACGATCAAACACATTGGGAGCTGTTGGATTCCTTGGGGATAGCAGAAG
+AATCAATGTTGCCATCACAAGAGCACGCAAACATTTAGCTTTGGTCTGTGACAGCTCGACTATATGCCA
+CAATACCTTCTTAGCAAGGCTTCTGCGTCATATTAGACACTTTGGTAGGGTGAAGCATGCAGAACCAGG
+TAGTTTTGGAGGATATGGACTTGGGATGAATCCAATATTACCTTCCATTAATTA
 Gm10    Glyma10g00210.1    CDS_6    16625    16782    -    1    9    
+15    25    32    GGTGTTAGCCCAACAGCTATTGCAGTGCAATCCCCTTATGTTGCTCAAGTA
+CAACTTTTGAGGGACAAGCTTGATGAATTTCCAGAAGCAGCAGGTACTGAGGTTGCAACCATTGACAGT
+TTTCAAGGTCGGGAAGCTGATGCAGTAATTTTATCCAT
 Gm10    Glyma10g00210.1    CDS_5    17595    17763    -    2    9    
+16    27    34    GCCTACTTGGATAACACAATGCCCGCTGCTATTGCTAGATACTAGAATGCC
+ATATGGAAGTCTGTCAGTTGGTTGTGAAGAGCATCTAGACCCGGCTGGAACAGGCTCACTTTATAATGA
+AGGAGAAGCTGAGATAGTTTTGCAGCATGTATTTTCCTTAATCTATGCC
 Gm10    Glyma10g00210.1    CDS_4    18046    19077    -    12    42  
+  91    145    173    GCGCAACTGTGAAGCTTTAATGCTGCTTCAGAAGAATGGTTTACGAA
+AGAAGAATCCTTCAATTTCTGTTGTTGCTACACTGTTTGGAGATGGGGAAGATGTTGCATGGCTTGAGA
+AAAATCATTTGGCTGACTGGGCAGAAGAAAAATTGGATGGAAGATTAGGAAATGAAACCTTTGATGATT
+CTCAGTGGAGAGCAATTGCAATGGGTTTGAATAAAAAGAGGCCTGTATTGGTTATCCAAGGCCCTCCTG
+GTACAGGCAAGACTGGTTTGCTCAAGCAACTTATAGCATGTGCTGTTCAGCAAGGTGAAAGGGTTCTTG
+TTACAGCACCTACTAATGCAGCTGTTGATAACATGGTAGAAAAGCTTTCAAATGTTGGATTAAATATAG
+TGCGGGTTGGAAATCCAGCTCGTATATCAAAAACAGTGGGATCAAAGTCTTTGGAAGAAATTGTAAATG
+CTAAGCTTGCAAGTTTTCGAGAAGAGTATGAGAGGAAGAAGTCAGATCTAAGAAAAGATCTAAGACATT
+GTTTAAGGGATGATTCACTAGCTTCAGGCATACGCCAACTTCTGAAGCAACTGGGAAGGTCACTGAAGA
+AAAAGGAAAAGCAGACCGTAATTGAAGTTCTGTCTAGTGCTCAAGTTGTGGTTGCCACTAATACTGGAG
+CAGCTGACCCTTTGGTTCGAAGGCTAGATACCTTTGATTTGGTTGTCATAGATGAAGCGGGACAGGCAA
+TTGAACCCTCTTGCTGGATTCCTATATTGCAGGGAAAGCGCTGCATTCTTGCTGGTGATCAATGCCAAC
+TTGCTCCTGTCATATTATCTAGAAAGGCCTTAGAAGTTGGTCTAGGAATATCTCTACTGGAGAGAGCTG
+CAACTTTGCATGAAGGGATTCTCACCACTAGGTTAACAACACAATACCGTATGAATGATGCAATTGCTA
+GTTGGGCTTCAAAGGAGATGTACGGAGGATTATTGAAGTCCTCTGAGACTGTCTTTTCTCATCTTCTAG
+TAGACTCTCCTTTTGTTAA
 Gm10    Glyma10g00210.1    CDS_3    21109    21392    -    4    8    
+30    42    52    GGACTTGGGGGAATGCATTTGGTGTTATTCAAGGTTGAAGGGAACCACCGG
+TTACCACCAACCACTCTTTCACCTGGAGACATGGTTTGTGTGAGAACATATGACAGCATGGGTGCAATT
+ACAACTTCTTGCATACAAGGATTTGTGAACAGTTTTGGGGATGATGGCTATAGTATTACAGTTGCTTTA
+GAGTCACGCCATGGTGATCCTACATTCTCTAAACTATTTGGGAAGAGTGTGCGCATTGACCGTATTCAA
+GGACTGGCTGATACACTTACTTATGA
 Gm10    Glyma10g00210.1    CDS_2    24354    24662    -    9    13   
+ 32    54    66    GCTCAGCATAGGGCGGTTGTGAGAAAGATAACGCAACCCAAGAGTGTCCA
+AGGCGTTTTAGGAATGGACTTCGAAAAGGTCAAAGCATTACAGCACAGGATTGACGAATTCACCACCCA
+TATGTCAGAACTACTCCGTATTGAAAGGGATGCTGAGTTGGAGTTTACTCAGGAGGAATTGGATGCTGT
+TCCTAAACCAGATGATACTTCTGATTCTTCAAAAACGATTGATTTCTTGGTTAGCCATAGCCAGCCTCA
+ACAAGAACTCTGCGACACCATTTGTAATTTAAACGCTATCAGTACCTCTACA
[download]

There are a total of 11 tab separated values in each line 1.) Chromosome (in this case Gm10) 2.) gene id(or Gene) 3.) Feature( which could be of many types CDS_\d or 5'UTR_\d or 3'UTR_\d e.t.c 4.) Start position of the gene 5.) End position 6.) Strand type + or - 7 to 11 ) different counts of different types 12) the Sequence.

Thanks graff for doing all the work. I'll try to see how your code works. But my other issue is I have 80 such files to compare with Methylation.gtf. I hope it can be done more efficiently. Thanks btw for all help appreciate it

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