Dear experts,
my problem is pretty tricky.
I want to change a file (see attached input.txt), according to another file (help.txt). The output that is desired is in output.txt. The example is attached.
Note that
-dashes should not be treated specially, they are considered normal characters, too.
-whatever is stripped from the first entry of the input.txt according to the help.txt should be stripped at the identical position in the second entry. (entries are separated by >)
I will really appreciate any help!
You will have a better response if you display a small sample in the post.
Some people do not or will not take the time to download your file and unzip it.
ok, you are right.
The files are as these:
input.txt:
>P1;baDHFR
structureX:baDHFR: 1: A:999 : B::::
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRD
GYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSN
YNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL
/
SKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQAEAGGMHTVCLSKSGQVYSFGCNDE
GALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVP
VVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAY
FTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSGGQHHTVCMDSEGKAYSLGRAEYGRLG
LGEGAEEKSIPTLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSPVEMMGKQLENRVVLSV
SSGGQHTVLLVKDKEQS*
>P1;hvDHFR
sequence:hvDHFR: 1: A: 999: B: :::
----AEPDVQFKLVLCGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTTRGTIKYNVWDTAGQEKFGGLRD
GYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSN
YNFEKPFLWLARKLVGDPNLEFVEMPALAPPEVVMDASLAAQYENDLKVAAETALPDEDDDL
/
-KKVKVSHSSHGQEKGLVLVLGQGDVGQLGLGEDIMERKRPALVTLPEGVVQVAAGGMHTVCLSDTGNIYTFGCNDE
GALGRETTEEGSEMVPGKVSLDERVVQVSAGDSHTAALTDDGAVYIWGSFRDNSGVIGLLEPMKKVTVPVKVPMKGP
VMKIASGNDHLVMLTTSGDLYTSGCGEQGQLGRVPELFANRGGRKGLLRLLIPQIVKVQSRGK---VHFTDAFCGAY
MTIAVSKEGHVYGFGLSNYHQLGTKLINTCFVPIKLTTFKNSTINWIGFSGGQHHTVCLDSAGKVYSLGRAEYGRLG
LGQGAEEKSEPTPVEGLDVAQVVACGASVSYAVTKQGSVYAWGMGTNLQLGTGEEDDEWSPVEMTGKQLENRIVLMV
ASGGQHTVLLVKDKQE-*
help.txt
>P1;1I2M
structureX:1I2M: 1 
+553 
::-1.00:-1.00
QVQFKLVLVGDGGTGKTTFVKRHLKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAI
IMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFL
WLARKLIGDPNLEFV/KVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQAEAGGMHTVCL
SKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLE
PMKKSMVPVQVQLDVPVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLK
HVRFQDAFCGAYFTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSGGQHHTVCMDSEG
KAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSP
VEMMGKQLENRVVLSVSSGGQHTVLLVKD*
output.txt
>P1;baDHFR
structureX:baDHFR: 1: A:999 : B::::
QVQFKLVLVGDGGTGKTTFVKRHLKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAI
IMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFL
WLARKLIGDPNLEF/VKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQAEAGGMHTVCL
SKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLE
PMKKSMVPVQVQLDVPVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLK
HVRFQDAFCGAYFTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSGGQHHTVCMDSEG
KAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSP
VEMMGKQLENRVVLSVSSGGQHTVLLVKD*
>P1;hvDHFR
sequence:hvDHFR: 1: A: 999: B: :::
DVQFKLVLCGDGGTGKTTFVKRHLKKYVATLGVEVHPLVFHTTRGTIKYNVWDTAGQEKFGGLRDGYYIQAQCAI
IMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFL
WLARKLVGDPNLEF/VKVSHSSHGQEKGLVLVLGQGDVGQLGLGEDIMERKRPALVTLPEGVVQVAAGGMHTVCL
SDTGNIYTFGCNDEGALGRETTEEGSEMVPGKVSLDERVVQVSAGDSHTAALTDDGAVYIWGSFRDNSGVIGLLE
PMKKVTVPVKVPMKGPVMKIASGNDHLVMLTTSGDLYTSGCGEQGQLGRVPELFANRGGRKGLLRLLIPQIVKVQ
-VHFTDAFCGAYMTIAVSKEGHVYGFGLSNYHQLGTKLINTCFVPIKLTTFKNSTINWIGFSGGQHHTVCLDSAG
KVYSLGRAEYGRLGLGQGAEEKSEPTPVEGLDVAQVVACGASVSYAVTKQGSVYAWGMGTNLQLGTGEEDDEWSP
VEMTGKQLENRIVLMVASGGQHTVLLVKD*
---------- Post updated at 12:13 PM ---------- Previous update was at 12:07 PM ----------
note that in the input file,
MAAQGEPQVQ....EDDDL
SKKVKVS....DKEQS*
----A...EDDD
-KK...KDKQE-*
each are in one line with no spaces, pasting at the forum did the misformating. I fixed by editing it.