Содержание
How to use grep to filter out lines starting with any of a set of keywords?
I have a large file (a chemical database), and I need to display only header records, which are defined as lines that don’t start with: ATOM , CONNECT , HETATM , TER , or END . I’m supposed to use grep to do this. Here’s a sample of the file (the entire file is here):
HEADER TRANSFERASE 15-OCT-12 4HKD TITLE CRYSTAL STRUCTURE OF HUMAN MST2 SARAH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE 3; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: SARAH DOMAIN, UNP RESIDUES 436-484; COMPND 5 SYNONYM: MAMMALIAN STE20-LIKE PROTEIN KINASE 2, MST-2, STE20-LIKE COMPND 6 KINASE MST2, SERINE/THREONINE-PROTEIN KINASE KRS-1, SERINE/THREONINE- COMPND 7 PROTEIN KINASE 3 36KDA SUBUNIT, MST2/N, SERINE/THREONINE-PROTEIN COMPND 8 KINASE 3 20KDA SUBUNIT, MST2/C; COMPND 9 EC: 2.7.11.1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: STK3, KRS1, MST2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: HT-PET28A KEYWDS HOMODIMERIZATION, HETERODOMERIZATION, SAV1, NEK2, RASSF, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.G.LIU,Z.B.SHI,Z.C.ZHOU REVDAT 1 04-SEP-13 4HKD 0 JRNL AUTH G.G.LIU,Z.B.SHI,Z.C.ZHOU JRNL TITL CRYSTAL STRUCTURE OF HUMAN MST2 SARAH DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 29481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.8685 - 3.3427 0.97 2878 149 0.1998 0.2322 REMARK 3 2 3.3427 - 2.6535 0.98 2711 175 0.2033 0.2452 REMARK 3 3 2.6535 - 2.3182 0.96 2660 155 0.1968 0.2148 REMARK 3 4 2.3182 - 2.1063 0.94 2620 114 0.1875 0.2318 REMARK 3 5 2.1063 - 1.9553 0.91 2533 113 0.1909 0.2295 REMARK 3 6 1.9553 - 1.8400 0.91 2476 143 0.1883 0.2137 REMARK 3 7 1.8400 - 1.7479 0.90 2465 128 0.1840 0.2029 REMARK 3 8 1.7479 - 1.6718 0.90 2446 130 0.1783 0.2144 REMARK 3 9 1.6718 - 1.6074 0.90 2419 129 0.1864 0.2400 REMARK 3 10 1.6074 - 1.5520 0.90 2487 120 0.1938 0.2588 REMARK 3 11 1.5520 - 1.5030 0.85 2289 141 0.1993 0.2471 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1771 REMARK 3 ANGLE : 1.179 2367 REMARK 3 CHIRALITY : 0.083 255 REMARK 3 PLANARITY : 0.006 317 REMARK 3 DIHEDRAL : 14.379 737 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-12. REMARK 100 THE RCSB ID CODE IS RCSB075574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29548 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 How to filter out lines of a command output that occur in a text file?
Let’s say we have a text file of forbidden lines forbidden.txt . What is a short way to filter all lines of a command output that exist in the text file?
cat input.txt | exclude-forbidden-lines forbidden.txt | sort 1 Answer 1
$ grep -v -x -F -f forbidden.txt input.txt That long list of options to grep means
- -v Invert the sense of the match, i.e. look for lines not matching.
- -x When matching a pattern, require that the pattern matches the whole line, i.e. not just anywhere on the line.
- -F When matching a pattern, treat it as a fixed string, i.e. not as a regular expression.
- -f Read patterns from the given file ( forbidden.txt ).
Then pipe that to sort or whatever you want to do with it.
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